diff --git a/tests/test_compare_vcfs.py b/tests/test_compare_vcfs.py index 6d288ac..dd428f3 100644 --- a/tests/test_compare_vcfs.py +++ b/tests/test_compare_vcfs.py @@ -99,20 +99,21 @@ def test_both_biallelic_same_alleles_different_order(): assert np.array_equal(actual, expected) -def test_biallelic_monoallelic(): +def test_both_biallelic_different_alleles(): ds1 = make_test_case() ds2 = ds1.copy(deep=True) # At the first site, one allele is shared. + ds2.variant_allele[0] = xr.DataArray([b'C', b'G']) + ds2.call_genotype[0] = xr.DataArray([[0, 1], [1, 0]]) # At the second site, no allele is shared. - for i in np.arange(ds2.variant_contig.size): - ds2.variant_allele[i] = xr.DataArray([b'C', b'']) - ds2.call_genotype[i] = xr.DataArray(np.zeros_like(ds2.call_genotype[i])) + ds2.variant_allele[1] = xr.DataArray([b'A', b'C']) + ds2.call_genotype[1] = xr.DataArray([[0, 1], [1, 0]]) # Subtest 1 _, actual = compare_vcfs.remap_genotypes(ds1, ds2) expected = xr.DataArray( [ - [[1, 1], [1, 1]], - [[2, 2], [2, 2]], + [[1, 2], [2, 1]], + [[2, 3], [3, 2]], ], dims=["variants", "samples", "ploidy"] ) @@ -121,29 +122,28 @@ def test_biallelic_monoallelic(): _, actual = compare_vcfs.remap_genotypes(ds2, ds1) expected = xr.DataArray( [ - [[1, 0], [0, 1]], - [[2, 1], [1, 2]], + [[2, 0], [0, 2]], + [[3, 2], [2, 3]], ], dims=["variants", "samples", "ploidy"] ) assert np.array_equal(actual, expected) -def test_both_biallelic_different_alleles(): +def test_biallelic_monoallelic(): ds1 = make_test_case() ds2 = ds1.copy(deep=True) # At the first site, one allele is shared. - ds2.variant_allele[0] = xr.DataArray([b'C', b'G']) - ds2.call_genotype[0] = xr.DataArray([[0, 1], [1, 0]]) # At the second site, no allele is shared. - ds2.variant_allele[1] = xr.DataArray([b'A', b'C']) - ds2.call_genotype[1] = xr.DataArray([[0, 1], [1, 0]]) + for i in np.arange(ds2.variant_contig.size): + ds2.variant_allele[i] = xr.DataArray([b'C', b'']) + ds2.call_genotype[i] = xr.DataArray(np.zeros_like(ds2.call_genotype[i])) # Subtest 1 _, actual = compare_vcfs.remap_genotypes(ds1, ds2) expected = xr.DataArray( [ - [[1, 2], [2, 1]], - [[2, 3], [3, 2]], + [[1, 1], [1, 1]], + [[2, 2], [2, 2]], ], dims=["variants", "samples", "ploidy"] ) @@ -152,8 +152,8 @@ def test_both_biallelic_different_alleles(): _, actual = compare_vcfs.remap_genotypes(ds2, ds1) expected = xr.DataArray( [ - [[2, 0], [0, 2]], - [[3, 2], [2, 3]], + [[1, 0], [0, 1]], + [[2, 1], [1, 2]], ], dims=["variants", "samples", "ploidy"] )